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Consolidate analysis loading helpers#19

Merged
OrF8 merged 2 commits into
cleanup/reorganize-codebasefrom
cleanup/consolidate-analysis-helpers
Jun 28, 2026
Merged

Consolidate analysis loading helpers#19
OrF8 merged 2 commits into
cleanup/reorganize-codebasefrom
cleanup/consolidate-analysis-helpers

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@OrF8

@OrF8 OrF8 commented Jun 28, 2026

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Summary

  • adds shared helpers for explicit daily/weekly value selection
  • consolidates directed activity/static-edge CSV loading
  • consolidates filtering directed edges to activity-matrix users
  • removes repeated inverse-problem window input loading
  • preserves all scientific and fallback behavior

Window semantics

  • preprocessing, Fano, lagged, and null-model workflows use exact daily match with weekly fallback
  • inverse workflows use exact weekly match with daily fallback
  • unsupported window values retain their historical fallback behavior
  • no window normalization or new validation is introduced

Loading boundary

  • shared directed loading preserves activity index conversion and static-edge schema
  • shared directed filtering preserves row order, duplicate edges, self-loops, extra columns, and filtered indices
  • validation remains in each scientific caller
  • inverse-specific loaders remain separate because they normalize different schemas

Compatibility

  • existing public signatures are unchanged
  • Python 3.9 remains the supported baseline
  • notebooks require no edits
  • editable-package imports continue to work from external directories

Reproducibility

  • lagged synthetic arrays and numerical CSVs match before the refactor
  • null-model synthetic numerical CSVs match before the refactor
  • all RNG streams and global-state isolation behavior are unchanged
  • no real analysis or cached result was regenerated

Validation

  • ran the complete unittest suite
  • added direct tests for the shared helper module
  • characterized all daily, weekly, and unsupported-window dispatch cases
  • verified validation order and exception messages
  • parsed all source and notebook cells with the Python 3.9 grammar
  • compiled source and tests with Python 3.12
  • imported all affected modules from an external working directory
  • confirmed notebooks, metadata, dependencies, configuration, data, and results are unchanged
  • did not run real analysis cells

@OrF8 OrF8 self-assigned this Jun 28, 2026
@OrF8 OrF8 marked this pull request as ready for review June 28, 2026 11:38
@OrF8 OrF8 requested a review from noam-kimhi as a code owner June 28, 2026 11:38
@OrF8 OrF8 merged commit ab27a86 into cleanup/reorganize-codebase Jun 28, 2026
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@OrF8 OrF8 deleted the cleanup/consolidate-analysis-helpers branch June 28, 2026 11:38
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